The ex-Borussia Dortmund midfielder announced his decision on Twitter, although the Nigerian Football Federation has yet to respond.
Oliseh wrote: "Due to contract violations, lack of support, unpaid wages, benefits to my players, asst. coaches and myself, I resign as Super Eagles Chief Coach.
"I feel fortunate, blessed and eternally grateful for having had the honour to play, captain and coach this great nation of ours, Nigeria."
The 41 year-old was allegedly told to report to Shaibu Amodu - technical director of the NFF - and was not happy with the decision, prompting him to quit.
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